The effects of human-mediated habitat fragmentation on a sedentary woodland-associated species (rhinolophus hipposideros) at its range margin

Among the many anthropogenic modifications to earth\u27s ecosystems, habitat loss and degradation pose the most immediate threat to many biota. The predicted consequences of fragmented habitats include lower species diversity, smaller population sizes, disrupted gene flow, increased drift and inbreeding and increased differentiation between neighbouring populations; all of which are thought to be further enhanced in species with low dispersal abilities. These factors, especially when occurring in tandem, can lead to an increased risk of extinction. To examine the genetic consequences of habitat fragmentation we selected an isolated population of a sedentary woodland specialist species (Rhinolophus hipposideros) to act as an indicator of disruptions to landscape level connectivity. Based on 491 individuals from 37 colonies our results revealed the presence of a broad North-Range/South-Range differentiation within this species in Ireland; a finding supported across datasets (mtDNA and nuclear microsatellites) and analyses. Analyses of echolocation data and microsatellites suggested further differentiation of the northern-most colonies. A landscape genetics framework to assess the impact of habitat versus geographic distance on population differentiation showed that habitat features (at a five km resolution) were equally likely to be correlated with differentiation as geographic distance considered alone. Further differentiation of the geographically disjunct groups is likely to occur in the future. The viability of either group alone is uncertain given their restricted distribution, small population sizes (based on census data and N-e estimates) and isolation. Roost provision and habitat restoration in the geographic region separating the differentiated groups will be fundamental to the recolonization of this area and the reestablishment of connectivity between the regional groups

The effects of human-mediated habitat fragmentation on a sedentary woodland-associated species (rhinolophus hipposideros) at its range margin

Among the many anthropogenic modifications to earth's ecosystems, habitat loss and degradation pose the most immediate threat to many biota. The predicted consequences of fragmented habitats include lower species diversity, smaller population sizes, disrupted gene flow, increased drift and inbreeding and increased differentiation between neighbouring populations; all of which are thought to be further enhanced in species with low dispersal abilities. These factors, especially when occurring in tandem, can lead to an increased risk of extinction. To examine the genetic consequences of habitat fragmentation we selected an isolated population of a sedentary woodland specialist species (Rhinolophus hipposideros) to act as an indicator of disruptions to landscape level connectivity. Based on 491 individuals from 37 colonies our results revealed the presence of a broad North-Range/South-Range differentiation within this species in Ireland; a finding supported across datasets (mtDNA and nuclear microsatellites) and analyses. Analyses of echolocation data and microsatellites suggested further differentiation of the northern-most colonies. A landscape genetics framework to assess the impact of habitat versus geographic distance on population differentiation showed that habitat features (at a five km resolution) were equally likely to be correlated with differentiation as geographic distance considered alone. Further differentiation of the geographically disjunct groups is likely to occur in the future. The viability of either group alone is uncertain given their restricted distribution, small population sizes (based on census data and N-e estimates) and isolation. Roost provision and habitat restoration in the geographic region separating the differentiated groups will be fundamental to the recolonization of this area and the reestablishment of connectivity between the regional groups

Phylogeography and postglacial recolonization of Europe by Rhinolophus hipposideros: evidence from multiple genetic markers

The demographic history of Rhinolophus hipposideros (lesser horseshoe bat) was recon- structed across its European, North African and Middle-Eastern distribution prior to, during and following the most recent glaciations by generating and analysing a multi- marker data set. This data set consisted of an X-linked nuclear intron (Bgn; 543 bp), mitochondrial DNA(cytb-tRNA-control region; 1630 bp) and eight variable microsatel- lite loci for up to 373 individuals from 86 localities. Using this data set of diverse markers, it was possible to determine the species’ demography at three temporal stages. Nuclear intron data revealed early colonization into Europe from the east, which pre-dates the Quaternary glaciations. The mtDNA data supported multiple glacial refugia across the Mediterranean, the largest of which were found in the Ibero- Maghreb region and an eastern location (Anatolia/Middle East)–that were used by R. hipposideros during the most recent glacial cycles. Finally, microsatellites provided the most recent information on these species’ movements since the Last Glacial Maxi- mumand suggested that lineages that had diverged into glacial refugia, such as in the Ibero-Maghreb region, have remained isolated. These findings should be used to inform future conservation management strategies for R. hipposideros and show the power of using a multimarker data set for phylogeographic studies.Peer reviewe

Data from: Variable molecular markers for the order Mantophasmatodea (Insecta)

The recently discovered insect order Mantophasmatodea currently comprises 19 Southern African species. These mainly occur in allopatry, have high levels of colour polymorphism and communicate via species- and gender-specific vibratory signals. High levels of interspecific morphological conservatism mean that cryptic species are likely to be uncovered. These aspects of Mantophasmatodean biology make them an ideal group in which to investigate population divergence due to habitat-specific adaptation, sexual selection and potentially sensory speciation. Lack of appropriate genetic markers has thus far rendered such studies unfeasible. To address this need, the first microsatellite loci for this order were developed. Fifty polymorphic loci were designed specifically for Karoophasma biedouwense (Austrophasmatidae), out of which 23 were labelled and tested for amplification across the order using 2-3 individuals from 10 species, representing all four currently known families. A Bayesian COI topology was reconstructed and divergence dates within the order were estimated for the first time. Amplification success and levels of polymorphism were compared with genetic divergence and time since divergence. In agreement with studies on vertebrate taxa, both amplification and variability were negatively correlated with distance (temporal and genetic). The high number of informative loci will offer sufficient resolution for both broad level population genetic analysis and individual based pedigree or parentage analyses for most species in Austrophasmatidae, with at least some loci available for the other families. This resource will facilitate research into the evolutionary biology of this understudied but fascinating group

Screening and Biosecurity for White-Nose Fungus Pseudogymnoascus destructans (Ascomycota: Pseudeurotiaceae) in Hawai‘i1

International audienceIntroduced pathogens causing emerging infectious diseases (EIDs) are serious contemporary threats to animal, plant, and ecosystem health. The invasive fungus, Pseudogymnoascus destructans, has established populations of European origin in North America, resulting in mass mortality of several hibernating bat species. Extensive monitoring for this pathogen exists in Europe and North America, but limited screening is taking place elsewhere. We report results from cave surveys on Hawai‘i Island. Substrates in 10 lava-tube caves with elevations up to 3,045 m were swabbed providing samples for screening P. destructans. Interior cave air temperatures spanned temperatures suitable for the growth and survival of P. destructans. Using quantitative PCR, all 85 samples tested were negative for the presence of P. destructans. The biology of the Hawaiian hoary bat (Lasiurus cinereus semotus) in relation to its unusual use of high elevation caves is discussed because these bats could come into contact with P. destructans should it arrive in Hawai‘i. Large numbers of cave enthusiasts visit Hawaiian caves from across the world after having been inside caves elsewhere including areas with P. destructans. Thus, resource managers in Hawai‘i and other remote areas may want to consider the potential for P. destructans to arrive unintentionally via human activities. Biosecurity measures and periodic screening for P. destructans are especially important in Hawai‘i given the presence of high elevation caves with suitable temperatures for its growth. If P. destructans was introduced to Hawaiian caves, it could affect the local fauna but also act as a source population for colonisations elsewhere

Data from: Nuclear introns outperform mitochondrial DNA in inter-specific phylogenetic reconstruction: Lessons from horseshoe bats (Rhinolophidae: Chiroptera)

Despite many studies illustrating the perils of utilising mitochondrial DNA in phylogenetic studies, it remains one of the most widely used genetic markers for this purpose. Over the last decade, nuclear introns have been proposed as alternative markers for phylogenetic reconstruction. However, the resolution capabilities of mtDNA and nuclear introns have rarely been quantified and compared. In the current study we generated a novel ∼5 kb dataset comprising six nuclear introns and a mtDNA fragment. We assessed the relative resolution capabilities of the six intronic fragments with respect to each other, when used in various combinations together, and when compared to the traditionally used mtDNA. We focused on a major clade in the horseshoe bat family (Afro-Palaearctic clade; Rhinolophidae) as our case study. This old, widely distributed and speciose group contains a high level of conserved morphology. This morphological stasis renders the reconstruction of the phylogeny of this group with traditional morphological characters complex. We sampled multiple individuals per species to represent their geographic distributions as best as possible (122 individuals, 24 species, 68 localities). We reconstructed the species phylogeny using several complementary methods (partitioned Maximum Likelihood and Bayesian and Bayesian multispecies-coalescent) and made inferences based on consensus across these methods. We computed pairwise comparisons based on Robinson–Foulds tree distance metric between all Bayesian topologies generated (27,000) for every gene(s) and visualised the tree space using multidimensional scaling (MDS) plots. Using our supported species phylogeny we estimated the ancestral state of key traits of interest within this group, e.g. echolocation peak frequency which has been implicated in speciation. Our results revealed many potential cryptic species within this group, even in taxa where this was not suspected a priori and also found evidence for mtDNA introgression. We demonstrated that by using just two introns one can recover a better supported species tree than when using the mtDNA alone, despite the shorter overall length of the combined introns. Additionally, when combining any single intron with mtDNA, we showed that the result is highly similar to the mtDNA gene tree and far from the true species tree and therefore this approach should be avoided. We caution against the indiscriminate use of mtDNA in phylogenetic studies and advocate for pilot studies to select nuclear introns. The selection of marker type and number is a crucial step that is best based on critical examination of preliminary or previously published data. Based on our findings and previous publications, we recommend the following markers to recover phylogenetic relationships between recently diverged taxa (<20 My) in bats and other mammals: ACOX2, COPS7A, BGN, ROGDI and STAT5A

Bayesian tree files - 6-intron+mtDNA partitioned topology

Tree files for the Bayesian analysis (NEXUS format). All Bayesian analysis were conducted in BEAST v. 1.8. This is described in section 2.4 of the paper (2.4 Phylogenetic reconstruction). The files were generated using the software associated with BEAST: LogCombiner and TreeAnnotator as described in section 2.4. The LogCombiner files contain all trees generated from 3 independent runs with burn-in removed for each analysis (i.e. 27,000 trees); here called ‘LogC’ files. The TreeAnnotator files contain a single consensus topology generated from these 27,000 trees (a maximum clade credibility tree, keeping target node heights); here called ‘TAn’ files. ‘P’ in the file name simply stands for ‘partitioned’; however all phylogenetic analyses with more than one locus were partitioned whether this is stated in the file name or not. See Readme file section 3 for more informatio